When a teacher deletes a student submission, the submission isn't deleted from the database. If the assign has a time limit, the submission's timestarted is kept so the "time remaining" will use the previous submission time instead of the new one.

How to reproduce:

1. As admin, go to "Site administration > Plugins > Activity modules > Assignment settings" and enable "Enable timed assignments".
2. As teacher, create a new assignment with time limit enabled: Availability > Time limit. E.g. you can set it to 30 minutes.
3. Enrol a student in the course.
4. Login as the student and open the assign.
5. Add a new submission and submit it (depending on the assign settings it will be submitted automatically once you save it).
6. As teacher, open the assign and click "View all submissions".
7. Search the student and click "Edit > Remove submission".
8. As the student, open the assign. Check that the time remaining starts counting from the first time you started the assign, it wasn't resetted when the submission was deleted.

EDIT: It seems setting timestarted as NULL in the assign_submission database table isn't enough. When I do it manually in a local site then the timer is ok and displays the right time. But when the student submits the assignment, the message displayed in "Time remaining" is still using the previous time instead of the new one. E.g. in my case it says that I submitted the assign 3 days late when I submitted it early, because the original submission was created 3 days ago.